Harvest for Persian Gulf Species List Created 25 Dec 08:53

Stage: completed
Fetched: 25 Dec 08:53
Validated: 25 Dec 08:53
Deltas Created 25 Dec 08:53
Units Normalized: 25 Dec 09:06
Ancestry Built: 25 Dec 08:54
Nodes Matched: 25 Dec 09:06
Names Parsed: 25 Dec 08:54
New Models Stored: 25 Dec 08:54
Indexed: 25 Dec 09:06
Completed: 25 Dec 09:08
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 08:53:35 -0500 by logger.rb/56815
[START] [2019-12-25 08:53:35] logged process
[START] [2019-12-25 08:53:35] create_harvest_instance
[STOP] [2019-12-25 08:53:36] create_harvest_instance
[START] [2019-12-25 08:53:36] fetch_files
[STOP] [2019-12-25 08:53:36] fetch_files
[START] [2019-12-25 08:53:36] validate_each_file
[STOP] [2019-12-25 08:53:36] validate_each_file
[START] [2019-12-25 08:53:36] convert_to_csv
[CMD] [2019-12-25 08:53:36] /usr/bin/sort /app/public/converted_csv/persian_gulf_sp__refs_19578.csv > /app/public/converted_csv/persian_gulf_sp__refs_19578.csv_sorted
[CMD] [2019-12-25 08:53:37] /usr/bin/sort /app/public/converted_csv/persian_gulf_sp__nodes_19579.csv > /app/public/converted_csv/persian_gulf_sp__nodes_19579.csv_sorted
[CMD] [2019-12-25 08:53:38] /usr/bin/sort /app/public/converted_csv/persian_gulf_sp__occurrences_19580.csv > /app/public/converted_csv/persian_gulf_sp__occurrences_19580.csv_sorted
[CMD] [2019-12-25 08:53:38] /usr/bin/sort /app/public/converted_csv/persian_gulf_sp__measurements_19581.csv > /app/public/converted_csv/persian_gulf_sp__measurements_19581.csv_sorted
[STOP] [2019-12-25 08:53:39] convert_to_csv
[START] [2019-12-25 08:53:39] calculate_delta
[CMD] [2019-12-25 08:53:39] echo "0a" > /app/public/diff/persian_gulf_sp__refs_19578.diff
[CMD] [2019-12-25 08:53:40] tail -n +1 /app/public/converted_csv/persian_gulf_sp__refs_19578.csv >> /app/public/diff/persian_gulf_sp__refs_19578.diff
[CMD] [2019-12-25 08:53:40] echo "." >> /app/public/diff/persian_gulf_sp__refs_19578.diff
[CMD] [2019-12-25 08:53:41] echo "0a" > /app/public/diff/persian_gulf_sp__nodes_19579.diff
[CMD] [2019-12-25 08:53:42] tail -n +1 /app/public/converted_csv/persian_gulf_sp__nodes_19579.csv >> /app/public/diff/persian_gulf_sp__nodes_19579.diff
[CMD] [2019-12-25 08:53:42] echo "." >> /app/public/diff/persian_gulf_sp__nodes_19579.diff
[CMD] [2019-12-25 08:53:43] echo "0a" > /app/public/diff/persian_gulf_sp__occurrences_19580.diff
[CMD] [2019-12-25 08:53:44] tail -n +1 /app/public/converted_csv/persian_gulf_sp__occurrences_19580.csv >> /app/public/diff/persian_gulf_sp__occurrences_19580.diff
[CMD] [2019-12-25 08:53:44] echo "." >> /app/public/diff/persian_gulf_sp__occurrences_19580.diff
[CMD] [2019-12-25 08:53:45] echo "0a" > /app/public/diff/persian_gulf_sp__measurements_19581.diff
[CMD] [2019-12-25 08:53:46] tail -n +1 /app/public/converted_csv/persian_gulf_sp__measurements_19581.csv >> /app/public/diff/persian_gulf_sp__measurements_19581.diff
[CMD] [2019-12-25 08:53:46] echo "." >> /app/public/diff/persian_gulf_sp__measurements_19581.diff
[STOP] [2019-12-25 08:53:47] calculate_delta
[START] [2019-12-25 08:53:47] parse_diff_and_store
[INFO] [2019-12-25 08:53:48] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 08:53:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 08:53:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 08:53:51] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 08:53:58] Storing 2 References
[INFO] [2019-12-25 08:53:58] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 08:53:58] Average Time: 0.0
[INFO] [2019-12-25 08:53:58] Total Time: 1s
[INFO] [2019-12-25 08:53:58] Storing 2699 ScientificNames
[INFO] [2019-12-25 08:53:58] Processing group of 2699 in 3 groups of 1000
[INFO] [2019-12-25 08:54:00] Average Time: 0.383
[INFO] [2019-12-25 08:54:00] Total Time: 2s
[INFO] [2019-12-25 08:54:00] Storing 2699 Nodes
[INFO] [2019-12-25 08:54:00] Processing group of 2699 in 3 groups of 1000
[INFO] [2019-12-25 08:54:01] Average Time: 0.33
[INFO] [2019-12-25 08:54:01] Total Time: 2s
[INFO] [2019-12-25 08:54:01] Storing 1268 Occurrences
[INFO] [2019-12-25 08:54:01] Processing group of 1268 in 2 groups of 1000
[INFO] [2019-12-25 08:54:01] Average Time: 0.085
[INFO] [2019-12-25 08:54:01] Total Time: 1s
[INFO] [2019-12-25 08:54:01] Storing 2536 TraitsReferences
[INFO] [2019-12-25 08:54:01] Processing group of 2536 in 3 groups of 1000
[INFO] [2019-12-25 08:54:01] Average Time: 0.103
[INFO] [2019-12-25 08:54:01] Total Time: 1s
[INFO] [2019-12-25 08:54:01] Storing 2536 Traits
[INFO] [2019-12-25 08:54:01] Processing group of 2536 in 3 groups of 1000
[INFO] [2019-12-25 08:54:02] Average Time: 0.313
[INFO] [2019-12-25 08:54:02] Total Time: 1s
[INFO] [2019-12-25 08:54:02] Storing 2536 MetaTraits
[INFO] [2019-12-25 08:54:02] Processing group of 2536 in 3 groups of 1000
[INFO] [2019-12-25 08:54:02] Average Time: 0.113
[INFO] [2019-12-25 08:54:02] Total Time: 1s
[STOP] [2019-12-25 08:54:02] parse_diff_and_store
[START] [2019-12-25 08:54:02] resolve_keys
[INFO] [2019-12-25 08:54:15] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 08:54:17] traits to occurrences...
[INFO] [2019-12-25 08:54:18] traits to nodes (through occurrences)...
[INFO] [2019-12-25 08:54:18] Traits to sex term...
[INFO] [2019-12-25 08:54:19] Traits to lifestage term...
[INFO] [2019-12-25 08:54:20] MetaTraits to traits...
[INFO] [2019-12-25 08:54:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 08:54:21] Assocs to occurrences...
[INFO] [2019-12-25 08:54:21] Assocs to nodes...
[INFO] [2019-12-25 08:54:21] Assoc to sex term...
[INFO] [2019-12-25 08:54:21] Assoc to lifestage term...
[STOP] [2019-12-25 08:54:21] resolve_keys
[START] [2019-12-25 08:54:21] hold_for_later_1
[STOP] [2019-12-25 08:54:21] hold_for_later_1
[START] [2019-12-25 08:54:21] hold_for_later_2
[STOP] [2019-12-25 08:54:21] hold_for_later_2
[START] [2019-12-25 08:54:21] resolve_missing_parents
[STOP] [2019-12-25 08:54:25] resolve_missing_parents
[START] [2019-12-25 08:54:25] rebuild_nodes
[START] [2019-12-25 08:54:25] Flattener#flatten
[START] [2019-12-25 08:54:25] Flattener#study_resource
[START] [2019-12-25 08:54:25] Flattener#build_ancestry
[STOP] [2019-12-25 08:54:25] Flattener#build_ancestry
[INFO] [2019-12-25 08:54:25] 2699 ancestry keys
[START] [2019-12-25 08:54:25] build_node_ancestors
[INFO] [2019-12-25 08:54:25] old ancestors deleted.
[STOP] [2019-12-25 08:54:26] build_node_ancestors
[START] [2019-12-25 08:54:27] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:54:27] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:54:27] Flattener#flatten
[STOP] [2019-12-25 08:54:27] rebuild_nodes
[START] [2019-12-25 08:54:27] resolve_missing_media_owners
[STOP] [2019-12-25 08:54:27] resolve_missing_media_owners
[START] [2019-12-25 08:54:27] sanitize_media_verbatims
[STOP] [2019-12-25 08:54:27] sanitize_media_verbatims
[START] [2019-12-25 08:54:27] queue_downloads
[STOP] [2019-12-25 08:54:27] queue_downloads
[START] [2019-12-25 08:54:27] parse_names
[WARN] [2019-12-25 08:54:27] I see 2699 names which still need to be parsed.
[STOP] [2019-12-25 08:54:31] parse_names
[START] [2019-12-25 08:54:31] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 08:54:31] denormalize_canonical_names_to_nodes
[START] [2019-12-25 08:54:31] match_nodes
[START] [2019-12-25 08:54:31] map_all_nodes_to_pages
[STOP] [2019-12-25 09:06:20] map_all_nodes_to_pages
[INFO] [2019-12-25 09:06:20] 132 Unmatched nodes (of 2699)! That's too many to output. First 10: Philomachus (#62396575); Philomachus pugnax (#62396574); Limicola (#62396702); Limicola falcinellus (#62396701); Anas clypeata (#62396477); Anas penelope (#62396512); Anas strepera (#62396584); Anas querquedula (#62396636); Puffinus griseus (#62397566); Puffinus creatopus (#62397752)
[START] [2019-12-25 09:06:20] update_nodes
[STOP] [2019-12-25 09:06:21] update_nodes
[STOP] [2019-12-25 09:06:21] match_nodes
[START] [2019-12-25 09:06:21] reindex_search
[STOP] [2019-12-25 09:06:29] reindex_search
[START] [2019-12-25 09:06:29] normalize_units
[STOP] [2019-12-25 09:06:29] normalize_units
[START] [2019-12-25 09:06:29] calculate_statistics
[STOP] [2019-12-25 09:06:29] calculate_statistics
[START] [2019-12-25 09:06:29] complete_harvest_instance
[START] [2019-12-25 09:06:29] overall_tsv_creation
[INFO] [2019-12-25 09:06:29] Processing group of 2699 in 1 batches of 10000
[INFO] [2019-12-25 09:07:27] 1268 Traits (unfiltered)...
[INFO] [2019-12-25 09:07:40] 1268 Traits (filtered)...
[INFO] [2019-12-25 09:07:40] 0 Associations (filtered)...
[INFO] [2019-12-25 09:08:20] 6340 metadata added.
[INFO] [2019-12-25 09:08:20] 0 metadata added.
[INFO] [2019-12-25 09:08:20] Average Time: 87.07
[INFO] [2019-12-25 09:08:20] Total Time: 1m52s
[STOP] [2019-12-25 09:08:20] overall_tsv_creation
[INFO] [2019-12-25 09:08:20] Done. Check your files:
[INFO] [2019-12-25 09:08:21] (2699 lines) /app/public/data/persian_gulf_sp_/publish_nodes.tsv
[INFO] [2019-12-25 09:08:22] (13409 lines) /app/public/data/persian_gulf_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-25 09:08:22] (2699 lines) /app/public/data/persian_gulf_sp_/publish_scientific_names.tsv
[INFO] [2019-12-25 09:08:23] (1269 lines) /app/public/data/persian_gulf_sp_/publish_traits.tsv
[INFO] [2019-12-25 09:08:24] (6341 lines) /app/public/data/persian_gulf_sp_/publish_metadata.tsv
[STOP] [2019-12-25 09:08:24] complete_harvest_instance
[START] [2019-12-25 09:08:24] completed
[STOP] [2019-12-25 09:08:24] completed
[STOP] [2019-12-25 09:08:24] logged process, took 888.76
Latest Process

25 Dec 08:53 EXITED currently processing 0